The two finalists, Aalborg (AaB) and SonderjyskE, were each allocated 750 tickets for the match in Esbjerg on Wednesday evening.
During the first half, “the referee had to suspend the match for up to 15 minutes, when the AaB fans refused to stay in the designated seats and huddled together in violation of the Covid rules,” Sydjylland police said on Twitter.
Pictures show members of the Aalborg staff unsuccessfully encouraging their supporters to return to their designated seats.
Between 40 and 50 of the fans were expelled from the ground and put on a bus and sent back to Aalborg with a police escort.
The match resumed after 14 minutes and ended in a 2-0 victory for SonderjyskE, who won the competition for the first time.
The police also tweeted that they arrested some fans for letting off flares.
The increased crowd for the match represented a loosening of Denmark's earlier coronavirus rules limiting attendance at a football match to 500 with a minimum distance between them of two metres.
On Tuesday, the Danish government said it would allow 500 fans into each section of the stadium and that would have to keep one metre apart.
In Copenhagen, up to 10,500 fans will be able into Parken, Denmark's largest stadium which can hold 38,000, FC Copenhagen club communications manager Jes Mortensen told AFP on Tuesday.